Analyze file which require write access

[marcelo-moglie]

Try symbolic link for Kilosort

[znamensk]

Do you mean that you need to overwrite the Dataset the you are analyzing? I would call Dataset.from_flexilims, run the analysis - as long as you have permission on CAMP - then update the attributes and created property and call the update_flexilims method.

[ablot]

I think that kilosort does not require write access to the data file itself but must write its output in the same directory as the data. I want to try to create a folder in the processed data directory with a symbolic link to the dataset and see if kilosort is happy to use that.
We just tried to make sure that the linking works with Marcelo, but we did not have any ephys dataset to do the actual test.

[znamensk]

That's annoying. Which files must it save there? From my quick dig around the kilosort repo, it looks like both the temporary binary and the phy2 output can be at a custom path.

Maybe forking kilosort and making a pull request to set custom paths would be a more elegant solution, if it's not too complicated?

[ablot]

Maybe it's not an issue anymore. If we change the temporary "fast ssd" path and replace the output line https://github.com/MouseLand/Kilosort/blob/main/main_kilosort3.m#L50